Full wwpdb X-ray Structure Validation Report

May 23, 2020  03:27 pm BST

PDB ID : 6I7S

Title : Microsomal triglyceride transfer protein

Authors : Biterova, E.; Isupov, M.N.; Keegan, R.M.; Lebedev, A.A.; Ruddock, L.W. Deposited on : 2018-11-17

Resolution : 2.50 Å(reported)

This is a Full wwPDB X-ray Structure Validation Report for a publicly released PDB entry. We welcome your comments at [email protected]

A user guide is available at

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp

with specic help available everywhere you see the Oi symbol.

The following versions of software and data (seereferencesOi) were used in the production of this report:

MolProbity : 4.02b-467

Mogul : 1.8.5 (274361), CSD as541be (2020) Xtriage (Phenix) : 1.13

EDS : 2.11

buster-report : 1.1.7 (2018)

Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019) Refmac : 5.8.0158

CCP4 : 7.0.044 (Gargrove) Ideal geometry (proteins) : Engh & Huber (2001) Ideal geometry (DNA, RNA) : Parkinson et al. (1996) Validation Pipeline (wwPDB-VP) : 2.11

1 Overall quality at a glance

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The following experimental techniques were used to determine the structure: X-RAY DIFFRACTION

The reported resolution of this entry is 2.50 Å.

Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown in the following graphic. The table shows the number of entries on which the scores are based.

Metric Whole archive_{(#Entries) (#Entries, resolution range(Å))}Similar resolution

Rf ree 130704 4661 (2.50-2.50)

Clashscore 141614 5346 (2.50-2.50) Ramachandran outliers 138981 5231 (2.50-2.50) Sidechain outliers 138945 5233 (2.50-2.50) RSRZ outliers 127900 4559 (2.50-2.50)

The table below summarises the geometric issues observed across the polymeric chains and their t to the electron density. The red, orange, yellow and green segments on the lower bar indicate the fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria respectively. A grey segment represents the fraction of residues that are not modelled. The numeric value for each fraction is indicated below the corresponding segment, with a dot representing fractions <=5% The upper red bar (where present) indicates the fraction of residues that have poor t to the electron density. The numeric value is given above the bar.

Mol Chain Length Quality of chain

1 A 492

1 B 492

2 G 884

2 H 884

The following table lists non-polymeric compounds, carbohydrate monomers and non-standard residues in protein, DNA, RNA chains that are outliers for geometric or electron-density-t

crite-ria:

Mol Type Chain Res Chirality Geometry Clashes Electron density

5 PGE B 602 - - - X 5 PGE B 603 - - - X 7 PEG B 609 - - - X 7 PEG H 916 - - - X 7 PEG H 917 - - X -7 PEG H 918 - - - X 8 PE5 G 901 - - - X 8 PE5 H 901 - - - X

2 Entry composition

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There are 11 unique types of molecules in this entry. The entry contains 21452 atoms, of which 0 are hydrogens and 0 are deuteriums.

In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occu-pancy, the AltConf column contains the number of residues with at least one atom in alternate conformation and the Trace column contains the number of residues modelled with at most 2 atoms.

ˆ Molecule 1 is a protein called Protein disulde-isomerase.

Mol Chain Residues Atoms ZeroOcc AltConf Trace 1 A 461 Total_{3668 2351 602 706 9}C N O S 0 1 0 1 B 462 Total_{3676 2354 600 713 9}C N O S 0 1 0

There are 2 discrepancies between the modelled and reference sequences: Chain Residue Modelled Actual Comment Reference

A 17 MET - initiating methionine UNP P07237 B 17 MET - initiating methionine UNP P07237

ˆ Molecule 2 is a protein called Microsomal triglyceride transfer protein large subunit. Mol Chain Residues Atoms ZeroOcc AltConf Trace

2 G 863 Total_{6787 4299 1164 1296 28}C N O S 0 4 0 2 H 862 Total_{6757 4277 1162 1290 28}C N O S 0 2 0

There are 16 discrepancies between the modelled and reference sequences: Chain Residue Modelled Actual Comment Reference

G 11 MET - initiating methionine UNP P55157 G 12 HIS - expression tag UNP P55157 G 13 HIS - expression tag UNP P55157 G 14 HIS - expression tag UNP P55157 G 15 HIS - expression tag UNP P55157 G 16 HIS - expression tag UNP P55157 G 17 HIS - expression tag UNP P55157 G 18 MET - expression tag UNP P55157 H 11 MET - initiating methionine UNP P55157 H 12 HIS - expression tag UNP P55157 Continued on next page...

Continued from previous page...

Chain Residue Modelled Actual Comment Reference H 13 HIS - expression tag UNP P55157 H 14 HIS - expression tag UNP P55157 H 15 HIS - expression tag UNP P55157 H 16 HIS - expression tag UNP P55157 H 17 HIS - expression tag UNP P55157 H 18 MET - expression tag UNP P55157 ˆ Molecule 3 is CALCIUM ION (three-letter code: CA) (formula: Ca). Mol Chain Residues Atoms ZeroOcc AltConf

3 B 1 Total Ca_{1 1} 0 0

3 A 1 Total Ca_{1 1} 0 0

ˆ Molecule 4 is 1,2-ETHANEDIOL (three-letter code: EDO) (formula: C2H6O2).

Mol Chain Residues Atoms ZeroOcc AltConf

4 A 1 Total C O_{4 2 2} 0 0

4 A 1 Total C O_{4 2 2} 0 0

4 A 1 Total C O_{4 2 2} 0 0

4 A 1 Total C O_{4 2 2} 0 0

Continued from previous page...

Mol Chain Residues Atoms ZeroOcc AltConf

4 A 1 Total C O_{4 2 2} 0 0 4 B 1 Total C O_{4 2 2} 0 0 4 B 1 Total C O_{4 2 2} 0 0 4 B 1 Total C O_{4 2 2} 0 0 4 G 1 Total C O_{4 2 2} 0 0 4 G 1 Total C O_{4 2 2} 0 0 4 G 1 Total C O_{4 2 2} 0 0 4 G 1 Total C O_{4 2 2} 0 0 4 G 1 Total C O_{4 2 2} 0 0 4 G 1 Total C O_{4 2 2} 0 0 4 H 1 Total C O_{4 2 2} 0 0 4 H 1 Total C O_{4 2 2} 0 0 4 H 1 Total C O_{4 2 2} 0 0 4 H 1 Total C O_{4 2 2} 0 0 4 H 1 Total C O_{4 2 2} 0 0

Mol Chain Residues Atoms ZeroOcc AltConf 5 B 1 Total C O_{10 6 4} 0 0 5 B 1 Total C O_{10 6 4} 0 0 5 G 1 Total C O_{10 6 4} 0 0 5 H 1 Total C O_{10 6 4} 0 0 5 H 1 Total C O_{10 6 4} 0 0 5 H 1 Total C O_{10 6 4} 0 0

Mol Chain Residues Atoms ZeroOcc AltConf 6 B 1 Total O S_{5 4 1} 0 0 6 G 1 Total O S_{5 4 1} 0 0 6 G 1 Total O S_{5 4 1} 0 0 6 G 1 Total O S_{5 4 1} 0 0 6 G 1 Total O S_{5 4 1} 0 0 6 G 1 Total O S_{5 4 1} 0 0 6 G 1 Total O S_{5 4 1} 0 0 6 G 1 Total O S_{5 4 1} 0 0 6 H 1 Total O S_{5 4 1} 0 0 6 H 1 Total O S_{5 4 1} 0 0 6 H 1 Total O S_{5 4 1} 0 0

Mol Chain Residues Atoms ZeroOcc AltConf 7 B 1 Total C O_{7 4 3} 0 0 7 B 1 Total C O_{7 4 3} 0 0 7 G 1 Total C O_{7 4 3} 0 0 7 G 1 Total C O_{7 4 3} 0 0 7 H 1 Total C O_{7 4 3} 0 0 7 H 1 Total C O_{7 4 3} 0 0 7 H 1 Total C O_{7 4 3} 0 0 7 H 1 Total C O_{7 4 3} 0 0 7 H 1 Total C O_{7 4 3} 0 0

ˆ Molecule 8 is 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL (three-letter code: PE5) (formula: C18H38O9).

Mol Chain Residues Atoms ZeroOcc AltConf 8 G 1 Total C O_{27 18 9} 0 0 8 H 1 Total C O_{27 18 9} 0 0

ˆ Molecule 9 is 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (three-letter code: TRS) (formula: C4H12NO3).

Mol Chain Residues Atoms ZeroOcc AltConf 9 G 1 Total C N O_{8 4 1 3} 0 0

ˆ Molecule 10 is 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL (three-letter code: PE4) (formula: C16H34O8).

Mol Chain Residues Atoms ZeroOcc AltConf 10 H 1 Total C O_{24 16 8} 0 0

ˆ Molecule 11 is water.

Mol Chain Residues Atoms ZeroOcc AltConf

11 A 22 Total O_{22 22} 0 0

11 B 32 Total O_{32 32} 0 0

11 G 81 Total O_{81 81} 0 0

3 Residue-property plots

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These plots are drawn for all protein, RNA and DNA chains in the entry. The rst graphic for a chain summarises the proportions of the various outlier classes displayed in the second graphic. The second graphic shows the sequence view annotated by issues in geometry and electron density. Residues are color-coded according to the number of geometric quality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. A red dot above a residue indicates a poor t to the electron density (RSRZ > 2). Stretches of 2 or more consecutive residues without any outlier are shown as a green connector. Residues present in the sample, but not in the model, are shown in grey.

• Molecule 1: Protein disulde-isomerase Chain A:

MET ASP A19

• P20 • E21 • E22 • E23 • D24 • H25 • V26 • L27 • V28 • L29 • R30 N33 F34 • L38 • A39 • A40 • H41 • K42 • Y43 • L44 • L45 • V46 • E47 • L59 • E62 • Y63 • A64 • K65 • A66 • A67 • G68 K69 • L70 • K71 • A72 • E73 • G74 • S75 • E76 • I77 • R78 • L79 • A80 • Q93 Y94 I102 • K103 • F104 • F105 • R106 • N107 • G108 • D109 T110 • A111 • S112 • P113 • Y116 T117 A118 G119 R120 • E121 • A122 • D123 • D124 • I125 • V126 • N127 • W128 L129 • K130 • K131 R132 • T133 •

T139 L140 P141 S148 L149 V150 E151 E154 D163 S166 D167 F184 S190 K200 K207 K208 T221 I229 Q233 E239 Q243

T244 A245 P246 K247 H256 P262 V265 S273 K276 F282 F290 F304 A336 T340 C343 Q367 E378 D379 N387 Q402 N419 E433 A450

• D451 R452 Q475 D476 • G477 A478 • G479 •

ASP ASP ASP ASP LEU GLU ASP LEU GLU GLU ALA

GLU GLU PRO ASP MET GLU GLU ASP ASP ASP GLN LYS ALA VAL LYS ASP GLU LEU

• Molecule 1: Protein disulde-isomerase Chain B:

MET ASP ALA P20 E21

• E22 E23 D24 H25 • H41 K42 Y43 • L59 K69 L70 K71 • A72 • E73 G74 •

S75 R78 V82 Q93 R97 D109 S112 Y116 T117 A118 G119 R120 E121 I125 K130 K131 R132 T138

• T139 L140 • P141 • D142 G143 • A144 • A145 A146 • E154 F160 D163 V164 • E165 S166 A169 • L173 • Q174 E177 P183 • F184 G185 I186 • T187 • Y196 • Q197 L198 D199 G202 •

K207 T221 K222 I229 K230 Q233 E239 E242 A245 P246 G250 P262 V265

•

S273 F282 F290 E332 E333 L334

T335 A336 E337 R338 I339 T340 C343 G349 E362 D363 K366 Q367 K375 W396 L403 F440 L443 N458 A478 G479

•

D480

•

D481 ASP ASP LEU GLU ASP LEU GLU GLU ALA GLU GLU PRO ASP MET GLU GLU ASP ASP ASP GLN LYS ALA VAL LYS ASP GLU LEU

• Molecule 2: Microsomal triglyceride transfer protein large subunit Chain G:

MET HIS HIS HIS HIS HIS HIS MET VAL K20

• G21 • H22 • D31 R32 L33 L36 R46 G47 • K48 G49 •

S252 K255 R266 S269 G270 K271 Q272 I276 I277 V280 K283 S296 H297 C298 S305 W308 R312 D318 S321 I347 E351 N352 K353 E354 V355 L356 L359 V360 D361 S369 D377 F381 D384

•

I387 Q390 E391 R392

Y395 L411 K414 S421 I424 M429 R437 G444 C445 K446 L447 L456 I457 L461

• E462 • D469 • L474 •

K491 E497 I500 L513 D518 K521 K533 T538 I547 N559 L567 P568 Q569 N572 Q580 M587 P588 A589

S590 K591 I592 V593 R594 R595 M600 V601 A602 R607 F608 S609 R610 I642 K656 A657 E672 A673 L674 I675 T678 L696 L701 N708 G709 Y710 S711 D712 L713

•

M714 S715 K716 M717 LEU SER ALA S721 V728 E740 L747 N750 L757 A758 I759 L769

R772 N780 R781 V785 S794 S804 T805 E806 S820 Q821 Y822 P823 M830 F840 L847 S848 T849 R858 Q885 PRO ASP SER THR SER SER GLY TRP PHE

• Molecule 2: Microsomal triglyceride transfer protein large subunit Chain H:

MET HIS HIS HIS HIS HIS HIS MET VAL LYS G21

• H22 • L26 D31 R32 L33 T37 Y38 S39 K48 • D53 S60 D64 D76 L79 E90 E98 •

K99 K113 A118 T123 L124 K133 Y136 S137 Y138

• K149 I170 S171 H181 • Q182 • D183 •

K189 I196 Q206 S216 V217 T218 D224 S225 A232 F242 K247 S252 R266 L267 M268 S269 G270 K271 Q272 A273

• I276 V280 K283 Y284 • V290 H297 • C298 S305 W308 D318 S321 I347 E351 N352 K353 L356

L359 V360 S369 D377 D384 L394 Y395 S421 T427 V428 M429 I430 I431 T434 R437 N442 C445 L456 I457 E465

•

K466 K467 E468 D469 L481 E497 I500 R510 T517 D518 E519 V520 K521 R526 N531 I547 K558 M571

M587 P588 I592 V593 L597 K598 E599 P625 R626 R644 I654 G655 K656 A657 V665 I675 A676

•

E684 N685 L686 M692 L696 V699 Q700 L701 N708 G709 Y710

•

S711 D712 S715 K716 M717 LEU SER ALA SER G722

• D723 • P724 I725 • I735 L747 K748

A749 G755 G756 L757 A758 I759 S768

• L769 • W770 • Y771 • R772 • K779 N780 R781 V782 T783 V784 V785 T788 T791 S794 S795 T803 E806 S820 Q821 F840 L847 S848 R858 P869 L870 H871 N874 S875 Q885 • P886 •

4 Data and renement statistics

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Property Value Source

Space group P 1 Depositor

Cell constants

a, b, c, α, β, γ 77.54Å 105.59Å 112.27Å89.81◦ _76.95◦ _74.24◦ Depositor

Resolution (Å) 49.35  2.50_{49.35  2.50} Depositor_EDS % Data completeness

(in resolution range) 93.8 (49.35-2.50)93.8 (49.35-2.50) DepositorEDS

Rmerge 0.06 Depositor

Rsym (Not available) Depositor

< I/σ(I) >1 1.07 (at 2.51Å) Xtriage Renement program REFMAC 5.8.0238 Depositor

R, Rf ree 0.204 , 0.257_{0.204 , 0.257} Depositor_DCC

Rf ree test set 5414 reections (5.00%) wwPDB-VP

Wilson B-factor (Å2) 65.6 Xtriage

Anisotropy 0.143 Xtriage

Bulk solvent ksol(e/Å3), Bsol(Å2) 0.31 , 50.7 EDS

L-test for twinning2 _{< |L| > = 0.50, < L}2 _>= 0.33 Xtriage

Estimated twinning fraction No twinning to report. Xtriage

Fo,Fc correlation 0.96 EDS

Total number of atoms 21452 wwPDB-VP Average B, all atoms (Å2_{) 72.0 wwPDB-VP}

Xtriage's analysis on translational NCS is as follows: The largest o-origin peak in the Patterson function is 4.33% of the height of the origin peak. No signicant pseudotranslation is detected.

1_{Intensities estimated from amplitudes.}

2_{Theoretical values of < |L| >, < L}2_{>for acentric reections are 0.5, 0.333 respectively for untwinned datasets,}

5 Model quality

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5.1 Standard geometry

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Bond lengths and bond angles in the following residue types are not validated in this section: PGE, PE4, PE5, CA, EDO, SO4, TRS, PEG

The Z score for a bond length (or angle) is the number of standard deviations the observed value is removed from the expected value. A bond length (or angle) with |Z| > 5 is considered an outlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).

Mol Chain _{RMSZ #|Z| >5 RMSZ #|Z| >5}Bond lengths Bond angles 1 A 0.34 0/3756 0.68 0/5071 1 B 0.35 0/3764 0.68 0/5082 2 G 0.40 0/6897 0.71 0/9297 2 H 0.39 0/6868 0.72 0/9258 All All 0.38 0/21285 0.70 0/28708 There are no bond length outliers.

There are no bond angle outliers. There are no chirality outliers. There are no planarity outliers.

5.2 Too-close contacts

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In the following table, the Non-H and H(model) columns list the number of non-hydrogen atoms and hydrogen atoms in the chain respectively. The H(added) column lists the number of hydrogen atoms added and optimized by MolProbity. The Clashes column lists the number of clashes within the asymmetric unit, whereas Symm-Clashes lists symmetry related clashes.

Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes

1 A 3668 0 3593 35 0 1 B 3676 0 3588 41 0 2 G 6787 0 6921 89 0 2 H 6757 0 6899 90 0 3 A 1 0 0 0 0 3 B 1 0 0 0 0 4 A 20 0 30 4 0 4 B 12 0 18 0 0 4 G 24 0 36 1 0

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Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes

4 H 20 0 30 0 0 5 B 20 0 28 1 0 5 G 10 0 14 5 0 5 H 30 0 42 2 0 6 B 5 0 0 0 0 6 G 35 0 0 2 0 6 H 15 0 0 1 0 7 B 14 0 20 0 0 7 G 14 0 20 0 0 7 H 35 0 50 7 0 8 G 27 0 38 1 0 8 H 27 0 38 6 0 9 G 8 0 12 1 0 10 H 24 0 34 3 0 11 A 22 0 0 0 0 11 B 32 0 0 1 0 11 G 81 0 0 4 0 11 H 87 0 0 3 0 All All 21452 0 21411 252 0

The all-atom clashscore is dened as the number of clashes found per 1000 atoms (including hydrogen atoms). The all-atom clashscore for this structure is 6.

All (252) close contacts within the same asymmetric unit are listed below, sorted by their clash magnitude.

Atom-1 Atom-2 _{distance (Å)}Interatomic _{overlap (Å)}Clash 2:G:717:MET:CE 2:G:721:SER:CB 2.12 1.28 2:G:717:MET:CE 2:G:721:SER:HB3 1.69 1.19 2:H:79:LEU:CD2 2:H:276:ILE:HD11 1.72 1.18 2:G:717:MET:HE2 2:G:721:SER:CB 1.73 1.15 2:G:395:TYR:CE2 5:G:902:PGE:H22 1.92 1.04 2:H:780:ASN:ND2 8:H:901:PE5:H142 1.76 1.01 2:H:780:ASN:HD22 8:H:901:PE5:H142 1.21 1.00 2:G:717:MET:CE 2:G:721:SER:HB2 1.94 0.97 2:G:717:MET:HE2 2:G:721:SER:HB3 1.29 0.96 2:G:717:MET:HE3 2:G:721:SER:HB3 1.49 0.91 2:G:717:MET:HE2 2:G:721:SER:HB2 1.48 0.91 2:H:79:LEU:HD23 2:H:276:ILE:HD11 1.48 0.90 2:G:587:MET:HB3 2:G:588:PRO:HD2 1.53 0.90 2:G:717:MET:HE3 2:G:721:SER:CB 2.02 0.89 2:H:656:LYS:H 2:H:656:LYS:HE2 1.39 0.87

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Atom-1 Atom-2 _{distance (Å)}Interatomic _{overlap (Å)}Clash 2:G:822[B]:TYR:CD1 2:G:823[B]:PRO:HA 2.11 0.84 2:H:780:ASN:ND2 8:H:901:PE5:H151 1.93 0.84 2:H:587:MET:HB3 2:H:588:PRO:HD2 1.60 0.82 2:G:569:GLN:O 11:G:1001:HOH:O 1.99 0.80 2:G:429:MET:HE2 2:G:457:ILE:HG12 1.62 0.80 1:A:20:PRO:HG2 1:A:27:LEU:HD22 1.66 0.77 2:H:79:LEU:HD22 2:H:276:ILE:HD11 1.64 0.76 1:B:163:ASP:HB3 1:B:166:SER:HB2 1.69 0.74 2:H:79:LEU:CD2 2:H:276:ILE:CD1 2.60 0.74 2:H:79:LEU:HD23 2:H:276:ILE:CD1 2.17 0.74 2:H:429:MET:HE2 2:H:457:ILE:HG12 1.69 0.73 1:A:163:ASP:HB3 1:A:166:SER:HB2 1.71 0.72 1:A:19:ALA:N 1:A:20:PRO:CD 2.54 0.71 2:H:466:LYS:HB2 2:H:469:ASP:HB2 1.71 0.71 1:B:41:HIS:CE1 1:B:78:ARG:HG3 2.26 0.70 2:G:270:GLY:HA3 2:G:276:ILE:HD11 1.71 0.70 2:H:352:ASN:O 2:H:356:LEU:HB2 1.90 0.70 2:G:352:ASN:O 2:G:356:LEU:HB2 1.92 0.70 2:G:444:GLY:HA2 2:G:447:LEU:HD13 1.74 0.69 1:B:22:GLU:HG2 1:B:25:HIS:HA 1.72 0.69 2:G:717:MET:CE 2:G:721:SER:CA 2.71 0.68 2:H:526:ARG:HA 2:H:531:ASN:HD22 1.58 0.68 2:H:356:LEU:O 2:H:360:VAL:HG23 1.93 0.68 2:G:356:LEU:O 2:G:360:VAL:HG23 1.94 0.68 2:G:717:MET:HE3 2:G:721:SER:CA 2.24 0.67 1:A:262:PRO:HG2 1:A:265:VAL:HB 1.75 0.67 1:B:458:ASN:HB2 1:B:479:GLY:H 1.60 0.67 1:B:262:PRO:HG2 1:B:265:VAL:HB 1.76 0.66 2:G:847:LEU:O 2:G:848:SER:HB3 1.96 0.66 2:H:429:MET:CE 2:H:457:ILE:HG12 2.24 0.66 2:H:847:LEU:O 2:H:848:SER:HB3 1.96 0.66 2:H:517:THR:HB 6:H:906:SO4:O4 1.96 0.65 2:G:429:MET:CE 2:G:457:ILE:HG12 2.27 0.65 2:G:227:VAL:O 9:G:903:TRS:H11 1.97 0.64 1:B:174:GLN:HB3 1:B:222:LYS:HD2 1.78 0.64 2:H:780:ASN:HD22 8:H:901:PE5:C14 2.05 0.63 2:G:602:ALA:O 2:G:607:ARG:HD2 1.99 0.62 2:H:701:LEU:HD13 7:H:914:PEG:H42 1.82 0.62 1:A:150:VAL:HG13 4:A:603:EDO:H22 1.82 0.61 1:B:230:LYS:HA 1:B:233:GLN:HE21 1.64 0.61 1:B:458:ASN:H 1:B:478:ALA:HA 1.66 0.61

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Atom-1 Atom-2 _{distance (Å)}Interatomic _{overlap (Å)}Clash 2:G:444:GLY:CA 2:G:447:LEU:HD13 2.31 0.61 1:A:276:LYS:HE2 4:A:604:EDO:O1 2.00 0.61 2:G:36:LEU:HD12 2:G:36:LEU:N 2.16 0.61 2:H:60:SER:HB2 7:H:917:PEG:H21 1.82 0.61 2:H:434:THR:HG21 2:H:699:VAL:HG22 1.83 0.61 2:H:768:SER:HB2 2:H:771:TYR:HB2 1.83 0.60 2:H:99:LYS:NZ 10:H:902:PE4:H81 2.17 0.60 2:G:390:GLN:NE2 2:G:424:ILE:HD13 2.18 0.59 1:B:242:GLU:OE1 1:B:242:GLU:N 2.35 0.59 2:H:779:LYS:HE2 2:H:781:ARG:HD2 1.84 0.58 1:A:208:LYS:HG2 4:A:603:EDO:H12 1.86 0.58 2:H:276:ILE:O 2:H:280:VAL:HG23 2.03 0.58 2:G:381:PHE:CD1 2:G:414:LYS:HE3 2.39 0.58 1:A:387:ASN:HD22 1:A:419:ASN:ND2 2.02 0.57 2:G:780:ASN:HD22 8:G:901:PE5:H72 1.69 0.57 2:G:255:LYS:HE2 6:G:907:SO4:O1 2.04 0.57 2:H:840[A]:PHE:CD1 2:H:858:ARG:HG2 2.39 0.57 2:G:717:MET:CE 2:G:721:SER:HA 2.34 0.57 2:G:822[B]:TYR:CG 2:G:823[B]:PRO:HA 2.39 0.57 2:H:124:LEU:HB2 2:H:136:TYR:HB2 1.87 0.55 1:A:47:GLU:HG3 1:A:102:ILE:HD13 1.87 0.55 2:H:466:LYS:O 2:H:469:ASP:N 2.37 0.55 1:A:121:GLU:O 1:A:125:ILE:HD13 2.07 0.55 2:G:33:LEU:HD11 2:G:64:ASP:HB3 1.89 0.55 2:H:840[A]:PHE:HD1 2:H:858:ARG:HG2 1.72 0.55 1:B:245:ALA:HB3 1:B:246:PRO:HD3 1.89 0.55 1:A:245:ALA:HB3 1:A:246:PRO:HD3 1.89 0.55 2:G:390:GLN:HE21 2:G:424:ILE:HG21 1.72 0.54 2:G:840[A]:PHE:HD1 2:G:858:ARG:HG2 1.73 0.54 1:B:239:GLU:HB2 1:B:290:PHE:CZ 2.43 0.54 2:G:276:ILE:O 2:G:280:VAL:HG23 2.07 0.54 2:H:196:ILE:HD13 2:H:290:VAL:CG1 2.38 0.54 2:H:429:MET:CE 2:H:457:ILE:CG1 2.85 0.54 2:H:37:THR:HB 7:H:917:PEG:H31 1.90 0.54 2:G:587:MET:HB3 2:G:588:PRO:CD 2.33 0.54 2:G:717:MET:HE3 2:G:721:SER:HA 1.89 0.54 1:B:282:PHE:CZ 1:B:343:CYS:HB2 2.43 0.54 1:B:70:LEU:HD23 1:B:75:SER:HB3 1.89 0.53 2:H:48:LYS:HB2 2:H:247:LYS:NZ 2.24 0.53 2:H:780:ASN:HD22 8:H:901:PE5:H151 1.67 0.53 1:B:174:GLN:O 1:B:177:GLU:HG3 2.08 0.53

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Atom-1 Atom-2 _{distance (Å)}Interatomic _{overlap (Å)}Clash 1:B:121:GLU:O 1:B:125:ILE:HD13 2.08 0.53 2:G:429:MET:CE 2:G:457:ILE:CG1 2.87 0.53 2:H:196:ILE:HD13 2:H:290:VAL:HG11 1.90 0.53 2:G:124:LEU:HB2 2:G:136:TYR:HB2 1.92 0.52 1:A:184:PHE:HZ 1:A:229:ILE:HD13 1.73 0.52 1:A:282:PHE:CZ 1:A:343:CYS:HB2 2.44 0.52 1:A:239:GLU:HB2 1:A:290:PHE:CZ 2.45 0.52 1:A:30:ARG:HB3 1:A:33:ASN:HD21 1.75 0.52 2:G:580:GLN:HG2 11:G:1033:HOH:O 2.08 0.52 2:G:717:MET:HE1 2:G:721:SER:CB 2.31 0.52 2:H:847:LEU:O 2:H:848:SER:CB 2.56 0.52 2:G:31:ASP:OD1 2:G:266:ARG:HA 2.10 0.52 2:H:558:LYS:NZ 2:H:599:GLU:OE2 2.43 0.52 1:A:19:ALA:N 1:A:20:PRO:HD2 2.24 0.51 1:B:458:ASN:HB2 1:B:479:GLY:N 2.24 0.51 2:H:788:THR:HG1 2:H:803:THR:HG1 1.56 0.51 2:H:394:LEU:HB3 2:H:431:ILE:HD13 1.93 0.51 2:H:171:SER:O 2:H:196:ILE:HG21 2.11 0.51 2:H:283:LYS:HB3 11:H:1022:HOH:O 2.10 0.51 1:B:59:LEU:HD13 1:B:120:ARG:HD3 1.93 0.51 2:G:840[A]:PHE:CD1 2:G:858:ARG:HG2 2.45 0.51 1:B:184:PHE:HZ 1:B:229:ILE:HD13 1.76 0.50 2:H:785:VAL:HG22 2:H:806:GLU:HB3 1.93 0.50 2:H:26:LEU:HA 5:H:905:PGE:H1 1.93 0.50 1:A:77:ILE:HD11 1:A:132:ARG:NH1 2.27 0.50 2:G:717:MET:HE1 2:G:721:SER:HB2 1.86 0.50 2:H:33:LEU:HD11 2:H:64:ASP:HB3 1.94 0.49 1:A:304:PHE:HB2 2:G:609:SER:OG 2.12 0.49 2:G:592:ILE:HD12 2:G:595:ARG:NH1 2.28 0.49 1:A:190:SER:HB3 4:A:602:EDO:H22 1.93 0.48 1:A:378:GLU:CD 1:A:452:ARG:HH22 2.15 0.48 1:B:97:ARG:NH2 1:B:250:GLY:O 2.46 0.48 2:G:701:LEU:HD13 5:G:902:PGE:H2 1.94 0.48 2:H:189:LYS:HB3 2:H:216:SER:HB3 1.95 0.48 2:G:572:ASN:HB3 2:G:610:ARG:CD 2.44 0.48 2:G:747:LEU:HD22 2:G:794:SER:HB3 1.95 0.48 1:A:475:GLN:N 1:A:475:GLN:HE21 2.12 0.48 2:G:572:ASN:HB3 2:G:610:ARG:HD3 1.95 0.48 2:H:48:LYS:HB2 2:H:247:LYS:HZ2 1.79 0.48 2:G:189:LYS:HB3 2:G:216:SER:HB3 1.96 0.48 2:H:429:MET:HE1 2:H:457:ILE:CG1 2.44 0.48

Continued from previous page...

Atom-1 Atom-2 _{distance (Å)}Interatomic _{overlap (Å)}Clash 2:H:39:SER:HB2 7:H:917:PEG:H42 1.96 0.48 2:H:266:ARG:HD3 2:H:266:ARG:H 1.78 0.47 2:G:308:TRP:CD1 2:G:347:ILE:HG23 2.49 0.47 2:G:769:LEU:O 2:G:772:ARG:HD3 2.15 0.47 2:G:123:THR:HG21 11:G:1040:HOH:O 2.13 0.47 2:G:296:SER:HB2 11:G:1077:HOH:O 2.12 0.47 2:G:674:LEU:HD11 2:G:713:LEU:HD21 1.95 0.47 2:H:308:TRP:CD1 2:H:347:ILE:HG23 2.49 0.47 2:G:847:LEU:O 2:G:848:SER:CB 2.56 0.47 1:A:42:LYS:O 1:A:106:ARG:O 2.32 0.47 1:A:94:TYR:O 1:A:103:LYS:HE3 2.15 0.47 2:G:351:GLU:HB3 2:G:356:LEU:HD13 1.97 0.47 2:G:124:LEU:HD23 2:G:277:ILE:HG12 1.97 0.47 2:H:429:MET:HE1 2:H:457:ILE:HG13 1.97 0.47 2:H:521:LYS:HG2 2:H:547:ILE:HG12 1.97 0.47 2:H:395:TYR:CD2 7:H:914:PEG:H41 2.49 0.47 1:B:82:VAL:HA 11:B:704:HOH:O 2.14 0.46 2:G:384:ASP:OD1 2:G:387:ILE:HD11 2.15 0.46 2:H:32:ARG:HD3 11:H:1028:HOH:O 2.15 0.46 2:H:206:GLN:HB2 2:H:657:ALA:CB 2.45 0.46 2:H:99:LYS:HD2 2:H:99:LYS:HA 1.77 0.46 2:H:747:LEU:HD22 2:H:794:SER:HB3 1.97 0.46 1:B:335:THR:OG1 1:B:337:GLU:HG2 2.15 0.46 2:H:593:VAL:O 2:H:597:LEU:HG 2.16 0.46 2:H:242:PHE:HA 2:H:654:ILE:HD11 1.98 0.46 2:H:171:SER:O 2:H:196:ILE:CG2 2.63 0.45 1:B:154:GLU:O 1:B:207:LYS:HA 2.16 0.45 2:G:312:ARG:HH22 4:G:915:EDO:H21 1.80 0.45 2:H:625:PRO:HG2 11:H:1048:HOH:O 2.16 0.45 2:G:785:VAL:HG22 2:G:806:GLU:HB3 1.98 0.45 2:G:51:LEU:HD11 2:G:249:LYS:HD2 1.99 0.45 1:A:30:ARG:HB3 1:A:33:ASN:ND2 2.32 0.45 2:G:521:LYS:HG2 2:G:547:ILE:HG12 1.99 0.45 2:H:467:LYS:HE2 2:H:467:LYS:HB3 1.60 0.45 2:G:696:LEU:HD23 2:G:696:LEU:HA 1.87 0.44 2:H:467:LYS:HG2 2:H:468:GLU:OE2 2.17 0.44 1:A:336:ALA:O 1:A:340:THR:OG1 2.33 0.44 2:G:347:ILE:HG22 2:G:359:LEU:HD21 1.99 0.44 1:A:154:GLU:O 1:A:207:LYS:HA 2.17 0.44 1:B:230:LYS:HA 1:B:233:GLN:NE2 2.30 0.44 2:G:136:TYR:CZ 2:G:277:ILE:HD13 2.53 0.44

Continued from previous page...

Atom-1 Atom-2 _{distance (Å)}Interatomic _{overlap (Å)}Clash 2:G:708:ASN:O 2:G:712:ASP:HB3 2.17 0.44 2:G:395:TYR:HE2 5:G:902:PGE:H22 1.71 0.44 2:H:749:ALA:HA 2:H:791:THR:O 2.18 0.44 2:G:538:THR:HG23 6:G:906:SO4:O2 2.18 0.44 1:B:363:ASP:HB2 1:B:366:LYS:HB2 1.99 0.43 2:G:769:LEU:O 2:G:772:ARG:CD 2.66 0.43 1:B:396:TRP:CH2 2:H:875:SER:HB3 2.53 0.43 2:H:769:LEU:C 2:H:769:LEU:HD13 2.39 0.43 2:H:587:MET:HB3 2:H:588:PRO:CD 2.42 0.43 1:A:39:ALA:HA 1:A:107:ASN:ND2 2.33 0.43 1:B:116:TYR:CZ 1:B:118:ALA:HB3 2.53 0.43 2:H:31:ASP:OD1 2:H:266:ARG:HA 2.19 0.43 2:G:138:TYR:HE1 2:G:283:LYS:HB2 1.84 0.43 2:H:351:GLU:HB3 2:H:356:LEU:HD13 2.01 0.43 2:H:37:THR:HG22 7:H:917:PEG:H12 2.00 0.43 2:H:37:THR:CG2 7:H:917:PEG:H12 2.49 0.43 1:A:139:THR:O 1:A:141:PRO:HD3 2.19 0.43 2:H:526:ARG:HA 2:H:531:ASN:ND2 2.30 0.43 1:A:24:ASP:O 1:A:25:HIS:HB2 2.18 0.43 5:G:902:PGE:H2 5:G:902:PGE:H4 1.77 0.42 2:H:696:LEU:HA 2:H:696:LEU:HD23 1.88 0.42 2:G:381:PHE:CE1 2:G:414:LYS:HE3 2.54 0.42 1:A:116:TYR:CZ 1:A:118:ALA:HB3 2.54 0.42 2:H:735:ILE:HB 2:H:755:GLY:HA3 2.00 0.42 2:H:99:LYS:HZ2 10:H:902:PE4:H81 1.84 0.42 1:B:336:ALA:O 1:B:340:THR:OG1 2.35 0.42 2:G:361:ASP:OD2 2:G:392:ARG:NH1 2.52 0.42 2:G:182:GLN:HA 2:G:182:GLN:OE1 2.19 0.42 2:G:51:LEU:HD11 2:G:249:LYS:CD 2.49 0.42 2:G:772:ARG:HG2 2:G:820:SER:HA 2.01 0.42 2:H:347:ILE:HG22 2:H:359:LEU:HD21 2.01 0.42 2:H:481:LEU:HD21 2:H:510:ARG:HB2 2.01 0.42 1:B:367:GLN:HE21 1:B:367:GLN:HB2 1.69 0.42 2:H:780:ASN:HD21 8:H:901:PE5:H151 1.77 0.42 1:B:333:GLU:HB2 1:B:338:ARG:HG3 2.02 0.42 2:G:642:ILE:HD12 2:G:672:GLU:HG3 2.02 0.42 1:A:19:ALA:N 1:A:20:PRO:HD3 2.33 0.41 2:G:206:GLN:HB2 2:G:657:ALA:CB 2.49 0.41 1:A:47:GLU:HG3 1:A:102:ILE:CD1 2.48 0.41 1:B:139:THR:O 1:B:141:PRO:HD3 2.20 0.41 2:H:218:THR:HG23 2:H:232:ALA:HB2 2.02 0.41

Continued from previous page...

Atom-1 Atom-2 _{distance (Å)}Interatomic _{overlap (Å)}Clash 1:B:24:ASP:O 1:B:25:HIS:HB2 2.20 0.41 2:G:740:GLU:HG3 2:G:750:ASN:HD21 1.85 0.41 2:G:567:LEU:HB3 2:G:568:PRO:HD2 2.01 0.41 1:B:403:LEU:HD21 1:B:443:LEU:HD21 2.02 0.41 2:G:218:THR:HG23 2:G:232:ALA:HB2 2.03 0.41 2:G:352:ASN:OD1 2:G:354:GLU:HG2 2.21 0.41 1:A:129:LEU:O 1:A:132:ARG:HD3 2.19 0.41 1:A:256:HIS:CE1 2:G:600:MET:HE3 2.55 0.41 2:G:456:LEU:HA 2:G:456:LEU:HD12 1.94 0.41 2:G:559:ASN:HD22 2:G:559:ASN:HA 1.67 0.41 2:G:590:SER:HB3 2:G:594:ARG:NH2 2.35 0.41 2:H:708:ASN:O 2:H:712:ASP:HB3 2.20 0.41 2:H:757:LEU:HA 2:H:783:THR:O 2.20 0.41 2:H:427:THR:O 2:H:431:ILE:HD12 2.21 0.41 2:H:99:LYS:HZ1 10:H:902:PE4:H81 1.83 0.41 1:A:154:GLU:HA 1:A:208:LYS:HG3 2.03 0.41 2:G:69:TRP:CD1 2:G:276:ILE:HG13 2.56 0.41 1:B:132:ARG:HD3 1:B:132:ARG:HA 1.76 0.40 1:B:396:TRP:HH2 2:H:875:SER:HB3 1.85 0.40 1:B:349:GLY:HA2 5:B:603:PGE:H1 2.01 0.40 1:B:69:LYS:O 1:B:73:GLU:HB2 2.21 0.40 2:G:728:VAL:HG13 5:G:902:PGE:H5 2.02 0.40 2:H:456:LEU:HA 2:H:456:LEU:HD12 1.96 0.40 1:B:160:PHE:CD1 1:B:198:LEU:CD1 3.05 0.40 2:H:118:ALA:O 2:H:149:LYS:HE2 2.20 0.40 2:H:665:VAL:O 2:H:692:MET:HA 2.21 0.40 1:B:199:ASP:OD1 1:B:199:ASP:N 2.54 0.40 1:B:440:PHE:CE2 2:H:869:PRO:HB3 2.56 0.40 2:H:871:HIS:CE1 2:H:874:ASN:HB2 2.56 0.40 1:B:116:TYR:OH 1:B:119:GLY:O 2.26 0.40 5:H:903:PGE:H32 5:H:903:PGE:H52 1.54 0.40 There are no symmetry-related clashes.

5.3 Torsion angles

O

5.3.1 Protein backbone Oi

In the following table, the Percentiles column shows the percent Ramachandran outliers of the chain as a percentile score with respect to all X-ray entries followed by that with respect to entries of similar resolution.

The Analysed column shows the number of residues for which the backbone conformation was analysed, and the total number of residues.

Mol Chain Analysed Favoured Allowed Outliers Percentiles 1 A 460/492 (94%) 436 (95%) 22 (5%) 2 (0%) 34 54 1 B 461/492 (94%) 440 (95%) 19 (4%) 2 (0%) 34 54 2 G 863/884 (98%) 831 (96%) 31 (4%) 1 (0%) 51 73 2 H 860/884 (97%) 828 (96%) 28 (3%) 4 (0%) 29 48 All All 2644/2752 (96%) 2535 (96%) 100 (4%) 9 (0%) 41 61 All (9) Ramachandran outliers are listed below:

Mol Chain Res Type

1 A 23 GLU 1 A 166 SER 1 B 23 GLU 1 B 166 SER 2 H 716 LYS 2 G 76 ASP 2 H 76 ASP 2 H 795 SER 2 H 270 GLY 5.3.2 Protein sidechains Oi

In the following table, the Percentiles column shows the percent sidechain outliers of the chain as a percentile score with respect to all X-ray entries followed by that with respect to entries of similar resolution.

The Analysed column shows the number of residues for which the sidechain conformation was analysed, and the total number of residues.

Mol Chain Analysed Rotameric Outliers Percentiles 1 A 391/419 (93%) 368 (94%) 23 (6%) 19 37 1 B 393/419 (94%) 376 (96%) 17 (4%) 29 53 2 G 753/768 (98%) 708 (94%) 45 (6%) 19 37 2 H 750/768 (98%) 694 (92%) 56 (8%) 13 26 All All 2287/2374 (96%) 2146 (94%) 141 (6%) 18 35 All (141) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type 1 A 73 GLU 1 A 93 GLN 1 A 102 ILE 1 A 117 THR 1 A 121 GLU 1 A 132 ARG 1 A 148 SER 1 A 151 GLU 1 A 167 ASP 1 A 200 LYS 1 A 221 THR 1 A 233 GLN 1 A 243 GLN 1 A 247 LYS 1 A 273 SER 1 A 340 THR 1 A 367 GLN 1 A 379 ASP 1 A 402 GLN 1 A 419 ASN 1 A 433 GLU 1 A 451 ASP 1 A 475 GLN 1 B 42 LYS 1 B 71 LYS 1 B 93 GLN 1 B 112 SER 1 B 117 THR 1 B 130 LYS 1 B 131 LYS 1 B 132 ARG 1 B 199 ASP 1 B 221 THR 1 B 273 SER 1 B 332 GLU 1 B 337 GLU 1 B 340 THR 1 B 362 GLU 1 B 367 GLN 1 B 375 LYS 2 G 46 ARG 2 G 90 GLU 2 G 113 LYS

Continued from previous page... Mol Chain Res Type

2 G 123 THR 2 G 170 ILE 2 G 252 SER 2 G 269 SER 2 G 272 GLN 2 G 298 CYS 2 G 305 SER 2 G 318 ASP 2 G 321 SER 2 G 369 SER 2 G 377 ASP 2 G 384 ASP 2 G 411 LEU 2 G 421 SER 2 G 437 ARG 2 G 445 CYS 2 G 469 ASP 2 G 491 LYS 2 G 497 GLU 2 G 500 ILE 2 G 513 LEU 2 G 518 ASP 2 G 533 LYS 2 G 592 ILE 2 G 656 LYS 2 G 674 LEU 2 G 675 ILE 2 G 678 THR 2 G 710 TYR 2 G 711 SER 2 G 715 SER 2 G 716 LYS 2 G 717 MET 2 G 757 LEU 2 G 759 ILE 2 G 772 ARG 2 G 781 ARG 2 G 804 SER 2 G 830 MET 2 G 848 SER 2 G 849 THR 2 G 885 GLN

Continued from previous page... Mol Chain Res Type

2 H 32 ARG 2 H 53 ASP 2 H 90 GLU 2 H 113 LYS 2 H 123 THR 2 H 133 LYS 2 H 170 ILE 2 H 224 ASP 2 H 225 SER 2 H 252 SER 2 H 266 ARG 2 H 267 LEU 2 H 268 MET 2 H 272 GLN 2 H 298 CYS 2 H 305 SER 2 H 318 ASP 2 H 321 SER 2 H 353 LYS 2 H 369 SER 2 H 377 ASP 2 H 384 ASP 2 H 421 SER 2 H 434 THR 2 H 437 ARG 2 H 442 ASN 2 H 445 CYS 2 H 466 LYS 2 H 467 LYS 2 H 469 ASP 2 H 497 GLU 2 H 500 ILE 2 H 519 GLU 2 H 571 MET 2 H 592 ILE 2 H 626 ARG 2 H 644 ARG 2 H 656 LYS 2 H 675 ILE 2 H 684 GLU 2 H 686 LEU 2 H 711 SER

Continued from previous page... Mol Chain Res Type

2 H 715 SER 2 H 716 LYS 2 H 717 MET 2 H 757 LEU 2 H 759 ILE 2 H 768 SER 2 H 772 ARG 2 H 779 LYS 2 H 781 ARG 2 H 791 THR 2 H 820 SER 2 H 821 GLN 2 H 848 SER 2 H 858 ARG

Some sidechains can be ipped to improve hydrogen bonding and reduce clashes. All (24) such sidechains are listed below:

Mol Chain Res Type

1 A 224 ASN 1 A 243 GLN 1 A 367 GLN 1 A 419 ASN 1 A 475 GLN 1 B 41 HIS 1 B 224 ASN 1 B 233 GLN 1 B 367 GLN 1 B 402 GLN 2 G 334 GLN 2 G 390 GLN 2 G 559 ASN 2 G 569 GLN 2 G 685 ASN 2 G 744 GLN 2 G 780 ASN 2 H 272 GLN 2 H 334 GLN 2 H 442 ASN 2 H 531 ASN 2 H 780 ASN 2 H 821 GLN 2 H 856 GLN

5.3.3 RNA Oi

There are no RNA molecules in this entry.

5.4 Non-standard residues in protein, DNA, RNA chains

O

There are no non-standard protein/DNA/RNA residues in this entry.

5.5 Carbohydrates

O

There are no carbohydrates in this entry.

5.6 Ligand geometry

O

Of 51 ligands modelled in this entry, 2 are monoatomic - leaving 49 for Mogul analysis.

In the following table, the Counts columns list the number of bonds (or angles) for which Mogul statistics could be retrieved, the number of bonds (or angles) that are observed in the model and the number of bonds (or angles) that are dened in the Chemical Component Dictionary. The Link column lists molecule types, if any, to which the group is linked. The Z score for a bond length (or angle) is the number of standard deviations the observed value is removed from the expected value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).

Mol Type Chain Res Link _{Counts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2}Bond lengths Bond angles

7 PEG H 918 - 6,6,6 0.16 0 5,5,5 0.04 0 4 EDO G 912 - 3,3,3 0.07 0 2,2,2 0.16 0 4 EDO A 606 - 3,3,3 0.09 0 2,2,2 0.19 0 5 PGE H 903 - 9,9,9 0.18 0 8,8,8 0.27 0 5 PGE G 902 - 9,9,9 0.23 0 8,8,8 0.22 0 4 EDO H 909 - 3,3,3 0.13 0 2,2,2 0.35 0 6 SO4 G 908 - 4,4,4 0.51 0 6,6,6 0.27 0 10 PE4 H 902 - 23,23,23 0.23 0 22,22,22 0.16 0 7 PEG H 916 - 6,6,6 0.14 0 5,5,5 0.08 0 6 SO4 H 908 - 4,4,4 0.35 0 6,6,6 0.08 0 6 SO4 G 909 - 4,4,4 0.41 0 6,6,6 0.10 0 4 EDO G 913 - 3,3,3 0.10 0 2,2,2 0.13 0 4 EDO A 604 - 3,3,3 0.22 0 2,2,2 0.43 0 4 EDO B 605 - 3,3,3 0.25 0 2,2,2 0.41 0 8 PE5 H 901 - 26,26,26 0.29 0 25,25,25 0.14 0 4 EDO A 602 - 3,3,3 0.06 0 2,2,2 0.07 0 6 SO4 B 604 - 4,4,4 0.37 0 6,6,6 0.13 0 7 PEG H 917 - 6,6,6 0.29 0 5,5,5 0.24 0

Mol Type Chain Res Link _{Counts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2}Bond lengths Bond angles 4 EDO H 910 - 3,3,3 0.04 0 2,2,2 0.21 0 7 PEG B 609 - 6,6,6 0.19 0 5,5,5 0.14 0 4 EDO G 915 - 3,3,3 0.04 0 2,2,2 0.16 0 5 PGE H 904 - 9,9,9 0.18 0 8,8,8 0.17 0 4 EDO G 914 - 3,3,3 0.13 0 2,2,2 0.18 0 4 EDO G 911 - 3,3,3 0.26 0 2,2,2 0.45 0 6 SO4 G 907 - 4,4,4 0.33 0 6,6,6 0.06 0 4 EDO H 911 - 3,3,3 0.09 0 2,2,2 0.25 0 4 EDO B 607 - 3,3,3 0.08 0 2,2,2 0.41 0 4 EDO H 912 - 3,3,3 0.12 0 2,2,2 0.12 0 4 EDO A 603 - 3,3,3 0.30 0 2,2,2 0.92 0 6 SO4 H 907 - 4,4,4 0.37 0 6,6,6 0.22 0 6 SO4 G 906 - 4,4,4 0.29 0 6,6,6 0.21 0 4 EDO B 606 - 3,3,3 0.18 0 2,2,2 0.56 0 9 TRS G 903 - 7,7,7 0.13 0 9,9,9 0.36 0 7 PEG G 918 - 6,6,6 0.16 0 5,5,5 0.07 0 7 PEG H 915 - 6,6,6 0.13 0 5,5,5 0.09 0 4 EDO A 605 - 3,3,3 0.07 0 2,2,2 0.10 0 7 PEG H 914 - 6,6,6 0.10 0 5,5,5 0.13 0 5 PGE B 603 - 9,9,9 0.16 0 8,8,8 0.14 0 6 SO4 G 904 - 4,4,4 0.32 0 6,6,6 0.08 0 4 EDO G 916 - 3,3,3 0.29 0 2,2,2 0.66 0 6 SO4 G 905 - 4,4,4 0.43 0 6,6,6 0.15 0 6 SO4 H 906 - 4,4,4 0.45 0 6,6,6 0.32 0 7 PEG B 608 - 6,6,6 0.17 0 5,5,5 0.06 0 5 PGE B 602 - 9,9,9 0.20 0 8,8,8 0.13 0 8 PE5 G 901 - 26,26,26 0.34 0 25,25,25 0.16 0 6 SO4 G 910 - 4,4,4 0.36 0 6,6,6 0.06 0 5 PGE H 905 - 9,9,9 0.23 0 8,8,8 0.13 0 4 EDO H 913 - 3,3,3 0.10 0 2,2,2 0.20 0 7 PEG G 917 - 6,6,6 0.21 0 5,5,5 0.14 0

In the following table, the Chirals column lists the number of chiral outliers, the number of chiral centers analysed, the number of these observed in the model and the number dened in the Chemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns. '-' means no outliers of that kind were identied.

Mol Type Chain Res Link Chirals Torsions Rings

7 PEG H 918 - - 4/4/4/4

-4 EDO G 912 - - 0/1/1/1

-4 EDO A 606 - - 0/1/1/1

-5 PGE H 903 - - 5/7/7/7

Continued from previous page...

Mol Type Chain Res Link Chirals Torsions Rings

5 PGE G 902 - - 5/7/7/7 -4 EDO H 909 - - 1/1/1/1 -10 PE4 H 902 - - 14/21/21/21 -7 PEG H 916 - - 2/4/4/4 -4 EDO G 913 - - 1/1/1/1 -4 EDO A 604 - - 0/1/1/1 -4 EDO B 605 - - 0/1/1/1 -8 PE5 H 901 - - 15/24/24/24 -4 EDO A 602 - - 1/1/1/1 -7 PEG H 917 - - 2/4/4/4 -4 EDO H 910 - - 1/1/1/1 -7 PEG B 609 - - 2/4/4/4 -4 EDO G 915 - - 0/1/1/1 -5 PGE H 904 - - 5/7/7/7 -4 EDO G 914 - - 1/1/1/1 -4 EDO G 911 - - 1/1/1/1 -4 EDO H 911 - - 1/1/1/1 -4 EDO B 607 - - 1/1/1/1 -4 EDO H 912 - - 1/1/1/1 -4 EDO A 603 - - 0/1/1/1 -4 EDO B 606 - - 1/1/1/1 -7 PEG G 918 - - 0/4/4/4 -7 PEG H 915 - - 1/4/4/4 -4 EDO A 605 - - 1/1/1/1 -7 PEG H 914 - - 2/4/4/4 -5 PGE B 603 - - 7/7/7/7 -4 EDO G 916 - - 1/1/1/1 -9 TRS G 903 - - 0/9/9/9 -7 PEG B 608 - - 2/4/4/4 -5 PGE B 602 - - 5/7/7/7 -8 PE5 G 901 - - 15/24/24/24 -5 PGE H 905 - - 3/7/7/7 -4 EDO H 913 - - 0/1/1/1 -7 PEG G 917 - - 3/4/4/4

-There are no bond length outliers. There are no bond angle outliers. There are no chirality outliers.

All (104) torsion outliers are listed below: Mol Chain Res Type Atoms

10 H 902 PE4 C3-C4-O3-C5 5 G 902 PGE C3-C4-O3-C5 7 G 917 PEG O1-C1-C2-O2 5 G 902 PGE O2-C3-C4-O3 8 H 901 PE5 O2-C3-C4-O3 8 G 901 PE5 O3-C5-C6-O4 10 H 902 PE4 O6-C10-C9-O5 8 G 901 PE5 O6-C10-C9-O5 5 H 904 PGE O2-C3-C4-O3 8 G 901 PE5 O6-C11-C12-O7 7 H 917 PEG O2-C3-C4-O4 8 G 901 PE5 O1-C1-C2-O2 8 H 901 PE5 O3-C5-C6-O4 5 H 903 PGE O2-C3-C4-O3 4 H 909 EDO O1-C1-C2-O2 4 H 912 EDO O1-C1-C2-O2 5 B 603 PGE O2-C3-C4-O3 8 G 901 PE5 O2-C3-C4-O3 10 H 902 PE4 O4-C7-C8-O5 8 G 901 PE5 O4-C7-C8-O5 5 G 902 PGE O3-C5-C6-O4 7 H 914 PEG O1-C1-C2-O2 5 B 603 PGE O1-C1-C2-O2 8 G 901 PE5 O8-C15-C16-O52 5 B 603 PGE O3-C5-C6-O4 5 G 902 PGE C4-C3-O2-C2 5 H 903 PGE C3-C4-O3-C5 5 B 602 PGE O1-C1-C2-O2 4 G 913 EDO O1-C1-C2-O2 4 A 602 EDO O1-C1-C2-O2 4 G 916 EDO O1-C1-C2-O2 10 H 902 PE4 O7-C13-C14-O8 5 H 903 PGE O3-C5-C6-O4 8 G 901 PE5 O7-C13-C14-O8 8 H 901 PE5 O8-C15-C16-O52 7 H 915 PEG O2-C3-C4-O4 8 G 901 PE5 C9-C10-O6-C11 5 H 905 PGE O3-C5-C6-O4 4 H 910 EDO O1-C1-C2-O2 4 B 607 EDO O1-C1-C2-O2 10 H 902 PE4 O1-C1-C2-O2 8 H 901 PE5 C48-C50-O1-C1

Continued from previous page...

Mol Chain Res Type Atoms 8 G 901 PE5 C48-C50-O1-C1 10 H 902 PE4 O6-C11-C12-O7 7 H 918 PEG O1-C1-C2-O2 10 H 902 PE4 C8-C7-O4-C6 7 B 609 PEG C4-C3-O2-C2 10 H 902 PE4 C12-C11-O6-C10 7 H 918 PEG C1-C2-O2-C3 7 B 609 PEG C1-C2-O2-C3 8 G 901 PE5 C13-C14-O8-C15 8 H 901 PE5 C6-C5-O3-C4 7 H 916 PEG C1-C2-O2-C3 5 H 904 PGE C6-C5-O3-C4 5 B 603 PGE C1-C2-O2-C3 8 H 901 PE5 C9-C10-O6-C11 8 H 901 PE5 C11-C12-O7-C13 5 G 902 PGE C6-C5-O3-C4 10 H 902 PE4 C13-C14-O8-C15 7 B 608 PEG C4-C3-O2-C2 8 G 901 PE5 C4-C3-O2-C2 5 H 904 PGE C3-C4-O3-C5 4 A 605 EDO O1-C1-C2-O2 7 H 918 PEG C4-C3-O2-C2 8 H 901 PE5 C13-C14-O8-C15 5 H 905 PGE C4-C3-O2-C2 8 G 901 PE5 C12-C11-O6-C10 7 H 916 PEG C4-C3-O2-C2 5 B 602 PGE C1-C2-O2-C3 5 B 603 PGE C6-C5-O3-C4 5 B 602 PGE C6-C5-O3-C4 8 G 901 PE5 C7-C8-O5-C9 7 G 917 PEG C4-C3-O2-C2 5 H 904 PGE O1-C1-C2-O2 8 H 901 PE5 C2-C1-O1-C50 7 G 917 PEG C1-C2-O2-C3 5 B 602 PGE C3-C4-O3-C5 8 G 901 PE5 C10-C9-O5-C8 4 G 914 EDO O1-C1-C2-O2 10 H 902 PE4 O3-C5-C6-O4 8 H 901 PE5 O6-C10-C9-O5 8 H 901 PE5 C16-C15-O8-C14 5 B 603 PGE C4-C3-O2-C2 10 H 902 PE4 C16-C15-O8-C14

Continued from previous page...

Mol Chain Res Type Atoms 8 H 901 PE5 O1-C1-C2-O2 5 H 904 PGE O3-C5-C6-O4 7 H 917 PEG C4-C3-O2-C2 7 B 608 PEG C1-C2-O2-C3 5 B 602 PGE C4-C3-O2-C2 5 H 903 PGE C4-C3-O2-C2 10 H 902 PE4 O2-C3-C4-O3 7 H 914 PEG C4-C3-O2-C2 5 B 603 PGE C3-C4-O3-C5 10 H 902 PE4 C4-C3-O2-C2 8 H 901 PE5 O6-C11-C12-O7 4 H 911 EDO O1-C1-C2-O2 4 B 606 EDO O1-C1-C2-O2 5 H 905 PGE C6-C5-O3-C4 7 H 918 PEG O2-C3-C4-O4 5 H 903 PGE O1-C1-C2-O2 4 G 911 EDO O1-C1-C2-O2 8 H 901 PE5 C1-C2-O2-C3 10 H 902 PE4 C7-C8-O5-C9 8 H 901 PE5 O7-C13-C14-O8 There are no ring outliers.

17 monomers are involved in 34 short contacts:

Mol Chain Res Type Clashes Symm-Clashes

5 H 903 PGE 1 0 5 G 902 PGE 5 0 10 H 902 PE4 3 0 4 A 604 EDO 1 0 8 H 901 PE5 6 0 4 A 602 EDO 1 0 7 H 917 PEG 5 0 4 G 915 EDO 1 0 6 G 907 SO4 1 0 4 A 603 EDO 2 0 6 G 906 SO4 1 0 9 G 903 TRS 1 0 7 H 914 PEG 2 0 5 B 603 PGE 1 0 6 H 906 SO4 1 0 8 G 901 PE5 1 0 5 H 905 PGE 1 0

The following is a two-dimensional graphical depiction of Mogul quality analysis of bond lengths, bond angles, torsion angles, and ring geometry for all instances of the Ligand of Interest. In addition, ligands with molecular weight > 250 and outliers as shown on the validation Tables will also be included. For torsion angles, if less then 5% of the Mogul distribution of torsion angles is within 10 degrees of the torsion angle in question, then that torsion angle is considered an outlier. Any bond that is central to one or more torsion angles identied as an outlier by Mogul will be highlighted in the graph. For rings, the root-mean-square deviation (RMSD) between the ring in question and similar rings identied by Mogul is calculated over all ring torsion angles. If the average RMSD is greater than 60 degrees and the minimal RMSD between the ring in question and any Mogul-identied rings is also greater than 60 degrees, then that ring is considered an outlier. The outliers are highlighted in purple. The color gray indicates Mogul did not nd sucient equivalents in the CSD to analyse the geometry.

Ligand PE4 H 902

Bond lengths Bond angles

Torsions Rings

Ligand PE5 H 901

Bond lengths Bond angles

Torsions Rings

Ligand PE5 G 901

Bond lengths Bond angles

Torsions Rings

5.7 Other polymers

O

There are no such residues in this entry.

5.8 Polymer linkage issues

O

6 Fit of model and data

O

6.1 Protein, DNA and RNA chains

O

In the following table, the column labelled `#RSRZ> 2' contains the number (and percentage) of RSRZ outliers, followed by percent RSRZ outliers for the chain as percentile scores relative to all X-ray entries and entries of similar resolution. The OWAB column contains the minimum, median, 95th _{percentile and maximum values of the occupancy-weighted average B-factor per}

residue. The column labelled `Q< 0.9' lists the number of (and percentage) of residues with an average occupancy less than 0.9.

Mol Chain Analysed <RSRZ> #RSRZ>2 OWAB(Å2_{) Q<0.9}

1 A 461/492 (93%) 0.58 68 (14%) 2 2 38, 76, 149, 188 0 1 B 462/492 (93%) 0.16 23 (4%) 28 30 39, 72, 120, 167 0 2 G 863/884 (97%) 0.03 11 (1%) 77 79 34, 61, 107, 151 0 2 H 862/884 (97%) 0.18 24 (2%) 53 56 35, 64, 122, 167 0 All All 2648/2752 (96%) 0.20 126 (4%) 30 32 34, 66, 127, 188 0 All (126) RSRZ outliers are listed below:

Mol Chain Res Type RSRZ 1 A 77 ILE 11.4 1 B 72 ALA 7.6 1 A 79 LEU 7.2 1 A 72 ALA 6.7 1 A 111 ALA 6.7 1 A 104 PHE 6.5 1 A 78 ARG 6.3 1 A 20 PRO 6.2 1 A 45 LEU 6.1 1 A 76 GLU 6.0 1 B 479 GLY 5.8 1 A 43 TYR 5.7 2 H 770 TRP 5.6 1 A 19 ALA 5.6 1 B 140 LEU 5.5 1 A 105 PHE 5.5 1 A 80 ALA 5.3 1 A 479 GLY 5.3 1 A 103 LYS 5.2 1 A 29 LEU 5.1 1 A 113 PRO 5.1 Continued on next page...

Continued from previous page... Mol Chain Res Type RSRZ

1 A 26 VAL 5.1 1 A 126 VAL 5.1 1 A 108 GLY 5.0 2 H 885 GLN 4.8 1 A 67 ALA 4.7 1 A 63 TYR 4.6 2 H 182 GLN 4.5 1 A 121 GLU 4.4 2 G 462 GLU 4.4 2 H 297 HIS 4.4 1 A 122 ALA 4.3 1 A 75 SER 4.2 1 B 187 THR 4.1 1 A 25 HIS 4.1 1 A 478 ALA 4.1 2 G 461 LEU 4.1 1 B 144 ALA 4.1 1 A 44 LEU 4.0 1 A 74 GLY 4.0 1 A 120 ARG 4.0 1 A 125 ILE 3.9 1 B 143 GLY 3.9 1 A 46 VAL 3.9 1 A 27 LEU 3.8 1 A 112 SER 3.8 1 B 480 ASP 3.8 1 B 202 GLY 3.7 1 B 164 VAL 3.7 2 H 886 PRO 3.7 2 H 676 ALA 3.7 1 A 106 ARG 3.7 2 G 49 GLY 3.6 2 H 722 GLY 3.6 2 G 21 GLY 3.6 1 A 28 VAL 3.6 1 A 129 LEU 3.5 1 A 132 ARG 3.5 1 B 173 LEU 3.5 1 A 23 GLU 3.4 2 H 98 GLU 3.3 1 A 123 ASP 3.3 1 A 66 ALA 3.2

Continued from previous page... Mol Chain Res Type RSRZ

1 A 102 ILE 3.2 2 H 710 TYR 3.2 1 A 70 LEU 3.2 2 H 48 LYS 3.2 2 G 713 LEU 3.1 1 A 21 GLU 3.0 1 A 24 ASP 3.0 1 B 71 LYS 3.0 1 A 22 GLU 3.0 1 A 124 ASP 3.0 2 H 181 HIS 2.9 2 H 465 GLU 2.9 1 A 71 LYS 2.9 1 A 34 PHE 2.8 1 A 107 ASN 2.8 1 A 133 THR 2.8 2 H 138 TYR 2.8 1 A 59 LEU 2.8 1 A 41 HIS 2.7 1 B 21 GLU 2.6 1 A 127 ASN 2.6 1 A 65 LYS 2.6 1 A 130 LYS 2.6 2 H 772 ARG 2.6 1 A 47 GLU 2.6 1 A 40 ALA 2.6 1 A 110 THR 2.6 2 H 768 SER 2.6 2 G 20 LYS 2.5 1 B 141 PRO 2.5 2 G 474 LEU 2.5 2 H 22 HIS 2.4 1 A 69 LYS 2.4 1 B 186 ILE 2.3 1 A 450 ALA 2.3 1 A 73 GLU 2.3 2 H 273 ALA 2.3 2 H 723 ASP 2.3 2 G 22 HIS 2.3 1 A 42 LYS 2.3 1 B 169 ALA 2.2 2 H 769 LEU 2.2

Continued from previous page... Mol Chain Res Type RSRZ

1 A 476 ASP 2.2 1 B 43 TYR 2.2 2 H 183 ASP 2.2 2 H 21 GLY 2.2 1 A 38 LEU 2.2 2 H 771 TYR 2.2 1 B 138 THR 2.2 2 G 47 GLY 2.2 2 H 725 ILE 2.1 1 B 265 VAL 2.1 1 B 25 HIS 2.1 1 A 64 ALA 2.1 1 B 146 ALA 2.1 1 B 196 TYR 2.1 2 G 469 ASP 2.1 1 A 62 GLU 2.1 1 B 74 GLY 2.1 1 B 183 PRO 2.0 2 G 384 ASP 2.0 1 A 39 ALA 2.0 2 H 284 TYR 2.0

6.2 Non-standard residues in protein, DNA, RNA chains

O

There are no non-standard protein/DNA/RNA residues in this entry.

6.3 Carbohydrates

O

There are no carbohydrates in this entry.

6.4 Ligands

O

In the following table, the Atoms column lists the number of modelled atoms in the group and the number dened in the chemical component dictionary. The B-factors column lists the minimum, median, 95th _{percentile and maximum values of B factors of atoms in the group. The column}

labelled `Q< 0.9' lists the number of atoms with occupancy less than 0.9.

Mol Type Chain Res Atoms RSCC RSR B-factors(Å2) Q<0.9

4 EDO G 913 4/4 0.54 0.28 90,96,103,106 0 4 EDO G 912 4/4 0.55 0.21 72,78,81,83 4

Continued from previous page...

Mol Type Chain Res Atoms RSCC RSR B-factors(Å2) Q<0.9

7 PEG B 608 7/7 0.55 0.34 65,74,81,82 7 8 PE5 G 901 27/27 0.55 0.75 85,106,117,126 27 4 EDO H 910 4/4 0.62 0.21 94,98,102,104 0 4 EDO G 914 4/4 0.63 0.39 101,104,110,113 0 8 PE5 H 901 27/27 0.64 0.59 70,98,130,142 27 7 PEG H 916 7/7 0.66 0.51 89,101,106,106 7 4 EDO H 913 4/4 0.67 0.19 78,81,82,85 4 7 PEG H 918 7/7 0.69 0.40 71,78,87,95 7 4 EDO H 911 4/4 0.70 0.34 81,88,93,94 0 4 EDO A 604 4/4 0.71 0.20 71,84,84,92 0 4 EDO H 909 4/4 0.72 0.30 75,82,91,91 0 7 PEG B 609 7/7 0.72 0.77 60,69,80,81 7 4 EDO B 606 4/4 0.72 0.28 88,90,96,96 0 10 PE4 H 902 24/24 0.73 0.24 84,109,117,122 24 4 EDO H 912 4/4 0.73 0.34 98,103,111,115 0 4 EDO A 606 4/4 0.76 0.21 96,106,110,114 0 5 PGE B 602 10/10 0.76 0.59 67,76,90,93 10 5 PGE B 603 10/10 0.79 0.43 92,98,103,105 10 7 PEG H 917 7/7 0.80 0.24 66,71,78,78 7 7 PEG G 918 7/7 0.82 0.31 62,79,88,89 7 4 EDO G 911 4/4 0.82 0.14 64,79,85,91 0 4 EDO A 602 4/4 0.82 0.17 68,71,73,75 0 5 PGE H 904 10/10 0.83 0.32 67,78,96,99 10 5 PGE H 903 10/10 0.83 0.38 64,73,81,85 10 5 PGE G 902 10/10 0.83 0.42 65,69,88,88 10 7 PEG H 915 7/7 0.84 0.26 76,77,81,82 7 4 EDO A 605 4/4 0.84 0.21 62,72,73,76 0 4 EDO B 605 4/4 0.85 0.17 79,89,90,92 0 4 EDO A 603 4/4 0.85 0.54 64,66,67,68 0 6 SO4 G 906 5/5 0.85 0.25 64,65,74,75 5 4 EDO G 916 4/4 0.86 0.22 64,69,71,75 0 7 PEG H 914 7/7 0.87 0.23 77,89,90,91 0 5 PGE H 905 10/10 0.87 0.33 83,89,102,103 0 6 SO4 G 909 5/5 0.87 0.36 78,81,86,89 5 6 SO4 G 910 5/5 0.88 0.32 87,87,90,91 5 9 TRS G 903 8/8 0.88 0.27 51,62,66,74 0 4 EDO G 915 4/4 0.88 0.25 57,60,63,65 4 6 SO4 B 604 5/5 0.89 0.29 63,65,73,76 5 4 EDO B 607 4/4 0.90 0.18 69,72,76,78 4 6 SO4 G 907 5/5 0.91 0.18 76,78,85,87 5 7 PEG G 917 7/7 0.91 0.38 67,83,95,102 0 6 SO4 G 905 5/5 0.92 0.29 66,68,72,74 5

Continued from previous page...

Mol Type Chain Res Atoms RSCC RSR B-factors(Å2) Q<0.9

6 SO4 G 904 5/5 0.93 0.23 77,78,83,88 5 6 SO4 H 908 5/5 0.95 0.25 66,69,74,76 5 6 SO4 G 908 5/5 0.95 0.21 47,48,54,57 0 3 CA A 601 1/1 0.96 0.06 57,57,57,57 0 3 CA B 601 1/1 0.96 0.09 60,60,60,60 0 6 SO4 H 907 5/5 0.97 0.19 63,65,72,72 5 6 SO4 H 906 5/5 0.98 0.12 66,68,80,80 0

The following is a graphical depiction of the model t to experimental electron density of all instances of the Ligand of Interest. In addition, ligands with molecular weight > 250 and outliers as shown on the geometry validation Tables will also be included. Each t is shown from dierent orientation to approximate a three-dimensional view.

Electron density around PE5 G 901: 2mFo-DFc (at 0.7 rmsd) in gray

mFo-DFc (at 3 rmsd) in purple (negative)

Electron density around PE5 H 901: 2mFo-DFc (at 0.7 rmsd) in gray

mFo-DFc (at 3 rmsd) in purple (negative)

and green (positive)

Electron density around PE4 H 902: 2mFo-DFc (at 0.7 rmsd) in gray

mFo-DFc (at 3 rmsd) in purple (negative)

6.5 Other polymers

O